It won't hurt anything if you check it, but I wouldn't bother.
Your computer will automatically replace anything that's needed. Prefetch amounts to what your computer thinks you're going to use next.
Here's what Microsoft says about it
http://windows.microsoft.com/en-us/windows-vista/what-is-the-prefetch-folderAnd here's what the Wiki says
http://en.wikipedia.org/wiki/PrefetcherSo it may help speed startup, but isn't critical.